Genetic diversity and phylogeny of pearl millets [Pennisetum glaucum (L.) R. Br.] based on chloroplast trnL-F region

Local varieties of pearl millets in Saudi Arabia are heat- and drought-tolerant and are grown under various environments. Here, we evaluated the diversity of six local varieties based on sequencing and analysis of the trnL-F region of their chloroplast DNA that includes the genes of tRNA^Leu and tRNA^Phe and the intergenic spacer between them, trnL-F. The obtained sequences were 1171–1172 bp in length, including the complete sequences of the tRNA^Leu, trnL-F and tRNA^Phe regions. Three variable nucleotide sites were observed in the sequences of the Indian variety, whereas for each of the three varieties, Tihamah, Jazan, and Sayah, a single variable site was observed. The varieties, Yemeni and Baydhan, were identical for the entire analyzed sequence. The secondary structure of tRNA^Leu intron of Indian variety was distinct from the other five varieties, while Tihamah and Jazan were distinct in the secondary structure of trnL-F spacer. Additionally, Indian was distinct in the secondary structure of tRNA^Leu whereas Sayah and Jazan were distinct in the secondary structure of tRNA^Phe. Phylogenetic analysis with NCBI-retrieved accessions of the Pennisetum glaucum revealed close relationships between the investigated varieties with an exception of the Indian, which clustered separately from the other five varieties. The nucleotide polymorphism analysis revealed higher nucleotide diversity in the spacer between tRNA^Leu and tRNA^Phe than in the tRNA^Leu intron across the six local varieties. This study provides insights into the genetic diversity within local pearl millets, which is important for the conservation of the local varieties that exhibit exceptional adaptation to the harsh climate conditions in the Arabian Peninsula.

     

Genetic diversity within and among landraces of pearl millet (Pennisetum glaucum) under farmer management in West Africa

The influence of farmer management on pearl millet landrace diversity was determined by evaluating variation in individual farmers' populations from two villages in north-eastern Nigeria. The variability within and between landrace samples was estimated using variation at 163 amplified fragment length polymorphism marker (AFLP) loci. The data indicated that individual farmers' husbandry practices result in the isolation of their own group of ideotypes each in their own unique genetic backgrounds, thereby rendering landrace names inappropriate as indicators of a generic genetic identity. The implications of these findings for sampling strategies for genebanks and regional genetic evaluations are discussed.     

A minute P application contributes to a better establishment of pearl millet (Pennisetum glaucum (L.) R. Br.) seedling in P deficient soils

Many soils of the semi-arid tropics are deficient in P, and under such adverse conditions, the establishment of pearl millet seedlings is a critical step to achieve satisfactory crop stands. Phosphorus fertilizer is expensive for small holder farmers and is only applied at low rates, insufficient to give satisfactory crop stands. Methods are needed to enhance productivity at low rates of application. Here, we tested the hypothesis that a minute application of P at early seedling stage, equivalent to 125–500 g P/ha, would enhance the plant establishment under P-limiting conditions. We measured the minimum application of P needed to elicit a response of different genotypes. Pot experiments were conducted with pearl millet ( Pennisetum glaucum (L.) R. Br.) hybrids to measure the response to P placed close to the root system, 5 days after sowing (DAS), compared with a non-limiting P control (DAP). The placement treatments were 0, 0.25, 0.50, and 1.0 mg soluble P per seedling, applied as KH₂PO₄ solution. The localized placement of P increased biomass in all three soils tested. In one soil, plant biomass at 1000 μL (1 mg P) reached about 50% of the non limited control. If applied later than 19 DAS the placement had no effect on the plant biomass. Hybrid ICMP 451-P8 was more responsive than hybrid 81B-P6. Placement to 20 inbred lines of pearl millet increased biomass by an average of 105% compared with no placement with large genotypic variation. Although this work was not intended to be a way of applying P fertilizer to pearl millet under field conditions, it showed that applying minute amount of P to pearl millet seedling (equivalent to 125–500 g P/ha) enhanced their establishment and led to improved growth for at least 5–6 weeks after sowing. Further work is in progress to develop a feasible technology for field crops based on the results of this study.     

Delineating genetic inheritance and nonallelic genic interactions for grain iron and zinc concentration,yield and its attributes by generation mean analysis in pearl millet [Pennisetum glaucum (L.) R. Br.]

Genetic Resources and Crop Evolution - Pearl millet is a major staple cereal crop worldwide and genetic biofortification with enhanced grain iron (Fe) and zinc (Zn) concentrations are ongoing...     

Changes in the diversity and geographic distribution of cultivated millet (Pennisetum glaucum (L.) R. Br.) and sorghum (Sorghum bicolor (L.) Moench) varieties in Niger between 1976 and 2003

Changes in the diversity of landraces in centres of diversity of cultivated plants need to be assessed in order to monitor and conserve agrobioversity—a key-element of sustainable agriculture. This notably applies in tropical areas where factors such as increased populations, climate change and shifts in cropping systems are hypothesized to cause varietal erosion. To assess varietal erosion of staple crops in a country subjected to various anthropogenic and natural environmental changes, we carried out a study based on a comparison of the diversity of pearl millet and sorghum varieties collected in 79 villages spanning the entire cereal-growing zone of Niger over a 26 year period (1976–2003). For these two crops, the number, name and type of varieties according to important traits for farmers were considered at different spatial scales (country, region, village) at the two collection dates. The results confirmed the high diversity of millet and sorghum varieties in Niger. No erosion of varietal diversity was noted on a national scale during the period covered. Some changes were observed but were limited to the geographical distribution of certain varieties. This highlights that farmers’ management can preserve the diversity of millet and sorghum varieties in Niger despite recurrent and severe drought periods and major social changes. It also indicates that rainfed cereal cropping systems in Niger should remain to be based on millet and sorghum, while reinforcing farmers’ seed systems.     

Long-term nitrogen balance for pearl millet (Pennisetum glaucum L.) in an acid sandy soil of Niger

On acid sandy soils of Niger (West Africa) fertilizer N recovery by pearl millet (Pennisetum glaucum L.) is often more than 100 per cent in years with normal or above average rainfall. Biological nitrogen fixation (BNF) by N₂-fixing bacteria may contribute to the N supply in pearl millet cropping systems. For a long-term field experiment comprising treatments with and without mineral fertilizer (F) and with and without crop residue application (CR) a N balance sheet was calculated over a period of six years (1983-1988). After six years of successive millet cropping total N uptake (36-77 kg N ha^?1 yr^?1) was distinctly higher than the amount of fertilizer N applied (30 kg N ha^?1 yr^?1). The atmospheric input of NH₄-N and NO₃-N in the rainwater was about 2 kg N ha_?1 yr^?1, 70 % in the form of NH₄-N. Gaseous NH₃ losses from urea (broadcast, incorporated) were estimated from other experiments to amount to 36 % of the fertilizer N applied. Nitrogen losses by leaching (15 to > 25 kg N ha^?1 yr^?1) were dependent on the treatment and on the quantity and distribution of single rainfall events (>50 mm). Decline in total soil N content (0-60 cm) ranged from 15 to 48 kg N ha^?1 yr^?1. The long-term N balance (1983-1988) indicated an annual net gain between 6 (+CR-F) and 13 (+CR+F) kg N ha^?1 yr^?1. For the control (-CR-F) the long-term N balance was negative (10 kg N ha^?1 yr^?1). In the treatment with crop residues only, the N balance was mainly determined by leaching losses, whereas in treatments with mineral fertilizer application the N balance depended primarily on N removal by the millet crop. The annual net gain in the N balance increased from 7 kg ha^?1 with mineral fertilizer to 13 kg ha^?1 in the combination mineral fertilizer plus crop residues. In both the rhizosphere and the bulk soil (0-15 cm), between 9 and 45% of the total bacterial population were N₂-fixing (diazotrophic) bacteria. The increased N gain upon crop residue application was positively correlated with an increase in the number of diazotrophic and total bacteria. The data on bacterial numbers suggest that the gain of N in the longterm N balance is most likely due to an N input by biological nitrogen fixation. In addition, evidence exists from related studies that the proliferation of diazotrophs and total bacteria in the rhizosphere due to crop residue application stimulated root growth of pearl millet, and thus improved the phosphorus (P) acquisition in the P deficient soil.     

Genetic diversity and population structure of vegetable soybean (Glycine max (L.) Merr.) in China as revealed by SSR markers

Vegetable soybean is a kind of value-added specialty soybean serving as vegetable or snacks. Understanding the genetic structure of vegetable soybean is a key point for further utilization in breeding programs. In the present study, the genetic structure and diversity of 100 vegetable soybean accessions planted in China was analyzed using 53 simple sequence repeat (SSR) markers. A total of 296 alleles were detected with an average of 5.6 alleles per SSR locus. The polymorphism information content (PIC) values of SSR markers ranged from 0.074 to 0.831, with an average of 0.573. Nei’s genetic distance between accessions ranged from 0 to 0.9434 with an average of 0.6286. These vegetable soybean germplasms could be divided into 8 subgroups based on STRUCTURE analysis, or 11 subgroups based on unweighted pair group method with arithmetic average (UPGMA) cluster. Further comparison showed that the UPGMA subgroups and STRUCTURE subgroups were in fact highly consistent. Germplasms in each classified groups showed great consistency with their origins, seed coat colors or pedigrees. Genetic relationships among germplasm panels that initially came from different geographical regions were also analyzed. Germplasm panels from China Mainland, Taiwan Island and Japan were highly similar to each other with the similarities of over 98 %. Molecular data and cluster analysis also showed that germplasms from China Mainland are more diverse than those from other areas. These results gave us a deep insight into the genetic structure of vegetable soybeans in China and will help us to improve the breeding strategies.     

Natural occurrence of Pseudomonas aeruginosa,a dominant cultivable diazotrophic endophytic bacterium colonizing Pennisetum glaucum (L.) R. Br.

Endophytic microbial communities can have strong influence on the growth of their host plants. The present study reports a diazotrophic endophytic bacterial species that colonizes predominantly Pennisetum glaucum (pearl millet) and remains stabilized throughout the latter's various growth stages under field conditions. Qualitative and quantitative changes in the endophytic bacterial population structure were examined during the plant growth period at regular intervals of 7 days up to harvesting. DNA fingerprinting (ERIC-PCR) was used as a biomarker to track the identity of various isolates obtained at different time intervals. Identification of representative bacterial species corresponding to different ERIC types was made on the basis of 16S rRNA gene sequence analysis. Based on the colony forming unit (cfu) count of bacterial isolates observed at various growth stages, Pseudomonas aeruginosa PM389 was found to be the dominant diazotrophic species among the cultivable endophytes colonizing pearl millet. The population of P. aeruginosa was detected in the host 21 days after sowing (DAS), indicating its entry in plant roots from soil and suggesting its non-vertical transfer in pearl millet. Moreover, an upward migration of this dominant diazotrophic bacterial species to shoots was observed with the plant growth. Further evaluation of P. aeruginosa PM389 revealed its various plant growth promoting properties viz. nitrogen fixation, mineral phosphate solubilization, siderophore production and antagonistic properties.     

Genetic relationships and diversity among Brazilian cultivars and landraces of common beans (Phaseolus vulgaris L.) revealed by AFLP markers

The genetic variation and relationships among 31 accessions of Phaseolus vulgaris L., and two representatives of Vigna unguiculata L., were evaluated by AFLP analysis. A total of 263 DNA fragments across all materials were scored using nine primer combinations, averaging 32 per primer. More than 95% of the amplification products showed polymorphism, indicating high variation at the DNA level among these accessions. Pair-wise genetic similarity (Jaccard's coefficient) ranged from 0.553 to 0.840, with a mean of 0.765. Twenty-three accessions (70%) clustered into three groups. A majority of the commercial cultivars (91%) clustered within a single group, whereas the landraces were distributed along all the variation. An apparent correlation with phaseolin types was detected. Results of this study suggest that Brazilian landraces truly represent the overall genetic variability of Phaseolus vulgaris, confirming the multiple origins of these materials, and their potential as a source of variation for breeding programs.     

Genetic diversity within a range of cultivars and landraces of flax (Linum usitatissimum L.) as revealed by RAPDs

Analysis of the extent and distribution of genetic diversity incrop plants is essential for optimizing sampling and breedingstrategies. We used random amplified polymorphic DNA (RAPD)markers to assess genetic diversity and relationships in 22 Canadiancultivars, 29 selected world cultivars and 10 landraces of flax(Linum usitatissimum L.). RAPDvariation was generally low and more variation was detected among,than within, the investigated flax accessions. Based on 53 variableRAPD loci observed for the 61 accessions, the landraces had a lowerproportion of fixed recessive RAPD loci (0.427) (i.e.,more genetic variation) than all of the flax cultivars examined(0.492). The linseed cultivars had a lower proportion ofrecessive loci (0.469) than the fiber flax cultivars(0.529). Canadian linseed cultivars had a lower proportionof recessive loci (0.465) than the selected world flaxcultivars (0.512). A trend was also observed that the rateof loss in genetic variation in Canadian flax breeding programs overthe last fifty years was approximately two variable loci per 100 lociper 10 years. Clustering analyses based on similarity estimatesshowed that the fiber cultivars were more related (or similar toeach other) and were classified as a homogeneous group. All ofthe linseed cultivars were clustered in diverse groups with the ninelandrace accessions. Implications of these findings for flax breedingand germplasm management are discussed.     

Genetic diversity in cowpea [Vigna unguiculata (L.) Walp.] as revealed by RAPD markers

The present study, using RAPD analysis, was undertaken to characterize genetic variation in domesticated cowpea and its wild progenitor, as well as their relationships. The materials used consisted of 26 domesticated accessions, including accessions from each of the five cultivar-group, and 30 wild/weedy accessions, including accessions from West, East and southern Africa. A total of 28 primers generated 202 RAPD bands. One hundred and eight bands were polymorphic among the domesticated compared to 181 among wild/weedy cowpea accessions. Wild accessions were more diverse in East Africa, which is the likely area of origin of V. unguiculata var. spontanea. Var. spontanea is supposed to have spread westward and southward, with a loss of variability, loss counterbalanceed in southern Africa by introgressions with local perennial subspecies. Although the variabilty of domesticated cowpea was the highest ever recorded, cultivar-groups were poorly resolved, and several results obtained with isozyme data were not confirmed here. However primitive cultivars were more diverse than evolved cultivars, which still suggests two consecutive bottlenecks within domesticated cowpea evolution. As isozymes and AFLP markers, although with a larger number of markers, RAPD data confirmed the single domestication hypothesis, the gap between wild and domesticated cowpea, and the widespread introgression phenomena between wild and domesticated cowpea.     

Revealing genetic diversity and population structure in Pistachio (Pistacia vera L.) by SSR markers

Genetic Resources and Crop Evolution - Pistachio (Pistacia vera L.) is the only cultivated species in Pistacia genus and it is one of the most important species of hard-shelled fruits. Pistachio...     

Genetic diversity in Japanese aromatic rice (Oryza sativa L.) as revealed by nuclear and organelle DNA markers

Aromatic rice (Oryza sativa L.) cultivated in Japan is regionally differentiated by geographical distribution and characteristics. We aimed to characterize the lineage of Japanese aromatic rice using DNA markers. Based on analyses with nuclear SSR markers, we found that Japanese aromatic rice cultivars belong, with one exception, to japonica but showed some differences from authentic japonica and were divided into two clades that were distributed in western and eastern Japan, respectively. Further analyses with organelle markers showed that most of the cultivars in eastern Japan had cytoplasm characterized by tropical japonica, whereas most of those in western Japan had cytoplasm characterized by temperate japonica. We postulate that the ancestor of the cultivars in eastern Japan differs from those of the cultivars in western Japan, and that the two groups may have been separately introduced from Taiwan into Japan. The cytoplasm of aromatic rice cultivars in western Japan may have originated from tropical japonica and been substituted into the cytoplasm of temperate japonica through hybridization between tropical japonica as a male parent and temperate japonica as a female parent.     

Genetic diversity among Northwestern Argentinian cultivars of common bean (Phaseolus vulgaris L.) as revealed by RAPD markers

The genetic diversity of 10 commercial cultivars of common beans, developed in Northern Argentina was analyzed based on RAPD markers. Sixteen primers were assayed and among them only 4 showed polymorphisms. A similarity matrix was generated by applying three different association coefficients, Simple Matching, Jaccard and Dice. By the UPGMA method dendrograms were generated and also the principal coordinate analysis was performed. The similarity values found were higher than 40% suggesting that genetic diversity is low. Both cluster analysis and principal coordinates analysis associated commercial cultivars either to the Andean or the Mesoamerican gene pool.     

Genetic diversity in spring faba bean (Vicia faba L.) genotypes as revealed by high-throughput KASP SNP markers

Genetic Resources and Crop Evolution - Faba bean is one of the oldest legume crop grown around the world for its cheap source of protein and for being used in crop rotation with cereals to improve...     

Genetic diversity in accessions of lima bean (Phaseolus lunatus L.) determined from agro-morphological descriptors and SSR markers for use in breeding programs in Brazil

Genetic Resources and Crop Evolution - Lima bean (Phaseolus lunatus L.) have high genetic diversity, especially in Brazil, which has been maintained both on farms and in germplasm banks. Knowledge...     

Genetic diversity of anchote (Coccinia abyssinica (Lam.) Cogn.) from Ethiopia as revealed by ISSR markers

Anchote (Coccinia abyssinica) is plant endemic in Ethiopia with a high calcium content grown for its edible tuberous roots. In spite of its importance as food security crop, there is no information available on molecular genetic diversity of this crop. Therefore, the aim of this study was to assess genetic diversity within and among 12 populations of anchote using ISSR markers. Using nine ISSR primers, a total of 87 scorable bands was generated of which 74 were polymorphic. Within population diversity based on polymorphic bands ranged from 13.8 to 43.53 % with a mean of 33.05 %, Nei’s genetic diversity of 0.04–0.156 with a mean of 0.12, Shannon information index of 0.07–0.23 with a mean of 0.175 and analysis of molecular variation (AMOVA) of 51.4 % were detected. With all diversity parameters, the highest diversity was obtained from Gimbi, Bedele and Ale populations, whilst the lowest was from Manna. AMOVA showed a 48.56 % between populations variability and significantly lower than that of within population variation. Population differentiation with F_ST was 48.56 %. From Jaccard’s pairwise similarity coefficient, Decha and Nedjo were most related populations exhibiting 0.76 similarity and Manna and Nedjo were the most distantly related populations with similarity of 0.52. The only pentanucliotide primer used in the study, Primer 880 (GGAGA)3, showed a unique band in some individuals that appeared to be associated with morphological quantitative traits (lowest seed number, high protein content, largest fruit size and smallest vine length). Illubabor and Gimbi populations exhibited highest genetic diversity so that the populations should be considered as the primary sites in designing conservation areas for this crop.     

A phenotypic diversity analysis of foxtail millet (Setaria italica (L.) P. Beauv.) landraces of Chinese origin

A total of 23 381 foxtail millet landraces of Chinese origin were analysed for seven qualitative traits and four quantitative traits. The Shannon-Weaver diversity index was used to estimate the phenotypic diversity of each characteristic on the basis of administrative provinces and ecogeographical regions. Hierarchical analysis of variance indicated that most of the variation was due to differences among characteristics. Only the diversity indices for leaf color of seedlings, starch composition and 1000-grain weight showed significant differences among regions. In relative terms, a greater genetic divergence was found in some provinces of southern China, where foxtail millet is not a major crop.